Pathway Analysis for Squeezy
John Zhuang
2024-06-17
library(multiMiR)## Welcome to multiMiR.
##
## multiMiR database URL has been set to the
## default value: http://multimir.org/
##
## Database Version: 2.3.0 Updated: 2020-04-15library(clusterProfiler)## ## clusterProfiler v4.12.2 Learn more at https://yulab-smu.top/contribution-knowledge-mining/
##
## Please cite:
##
## S Xu, E Hu, Y Cai, Z Xie, X Luo, L Zhan, W Tang, Q Wang, B Liu, R Wang,
## W Xie, T Wu, L Xie, G Yu. Using clusterProfiler to characterize
## multiomics data. Nature Protocols. 2024, doi:10.1038/s41596-024-01020-z##
## Attaching package: 'clusterProfiler'## The following object is masked from 'package:multiMiR':
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## filterlibrary(org.Hs.eg.db)## Loading required package: AnnotationDbi## Loading required package: stats4## Loading required package: BiocGenerics##
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## colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
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## match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
## Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
## tapply, union, unique, unsplit, which.max, which.min## Loading required package: Biobase## Welcome to Bioconductor
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## Vignettes contain introductory material; view with
## 'browseVignettes()'. To cite Bioconductor, see
## 'citation("Biobase")', and for packages 'citation("pkgname")'.## Loading required package: IRanges## Loading required package: S4Vectors##
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## select## library(stringr)
library(ggplot2)0. Loading of Results
A. List of all Gene names in the dataset
gene.names = readRDS("data/derived/unique_gene_names.rds")B. Selected Features
results.squeezy = readRDS("data/sel_features/results_squeezy_coef.rds")
sel.features = results.squeezy
sel.features## $fold3
## $fold3$elasticnet_0.5
## $fold3$elasticnet_0.5$multigroup
## FN1.R2Gn G6PD.RPPA FASN.RPPA MSH6.RPPA TFRC.RPPA
## -0.05082038 1.79344129 1.83979725 0.52730351 0.15202426
##
## $fold3$elasticnet_0.5$onegroup
## FN1.R2Gn G6PD.RPPA FASN.RPPA PDCD4.RPPA MSH6.RPPA TFRC.RPPA
## -0.05082038 1.79344129 1.83979725 1.78890341 0.52730351 0.15202426
##
##
## $fold3$lasso
## $fold3$lasso$multigroup
## FN1.R2Gn G6PD.RPPA FASN.RPPA TFRC.RPPA
## -0.05082038 1.79344129 1.83979725 0.15202426
##
## $fold3$lasso$onegroup
## FASN.RPPA TFRC.RPPA
## 1.8397972 0.1520243
##
##
##
## $fold5
## $fold5$elasticnet_0.5
## $fold5$elasticnet_0.5$multigroup
## FN1.R2Gn G6PD.RPPA FASN.RPPA MSH6.RPPA TFRC.RPPA
## -0.05082038 1.79344129 1.83979725 0.52730351 0.15202426
##
## $fold5$elasticnet_0.5$onegroup
## FN1.R2Gn G6PD.RPPA FASN.RPPA PDCD4.RPPA MSH6.RPPA TFRC.RPPA
## -0.05082038 1.79344129 1.83979725 1.78890341 0.52730351 0.15202426
##
##
## $fold5$lasso
## $fold5$lasso$multigroup
## FN1.R2Gn G6PD.RPPA FASN.RPPA TFRC.RPPA
## -0.05082038 1.79344129 1.83979725 0.15202426
##
## $fold5$lasso$onegroup
## FASN.RPPA TFRC.RPPA
## 1.8397972 0.1520243
##
##
##
## $fold10
## $fold10$elasticnet_0.5
## $fold10$elasticnet_0.5$multigroup
## FN1.R2Gn G6PD.RPPA FASN.RPPA MSH6.RPPA TFRC.RPPA
## -0.05082038 1.79344129 1.83979725 0.52730351 0.15202426
##
## $fold10$elasticnet_0.5$onegroup
## FN1.R2Gn G6PD.RPPA FASN.RPPA PDCD4.RPPA MSH6.RPPA TFRC.RPPA
## -0.05082038 1.79344129 1.83979725 1.78890341 0.52730351 0.15202426
##
##
## $fold10$lasso
## $fold10$lasso$multigroup
## FN1.R2Gn G6PD.RPPA FASN.RPPA TFRC.RPPA
## -0.05082038 1.79344129 1.83979725 0.15202426
##
## $fold10$lasso$onegroup
## FASN.RPPA TFRC.RPPA
## 1.8397972 0.15202431. Convert microRNA to genes
Also remove the ending “.R2Gn” and “.RPPA” from gene names.
split.by.omic = function(variable.list) {
out.mRSG = variable.list[startsWith(variable.list, "hsa")]
out.R2Gn = variable.list[endsWith(variable.list, ".R2Gn")]
out.RPPA = variable.list[endsWith(variable.list, ".RPPA")]
out = list("miRNASeqGene" = out.mRSG,
"RNASeq2GeneNorm" = out.R2Gn,
"RPPAArray" = out.RPPA)
out
}multiomics.to.GENES = function(sel.features, full.search = F, table = "validated", drop.miRNA = F) {
multiomics.list = split.by.omic(sel.features)
# Convert miRNASeqGene to target GENE names
# Skipped and returns an empty list instead of the list of select features,
# or if microRNA features are explicitly dropped (drop.miRNA = T).
# (Usually done when the features has only a few miRNA and unable to target any genes)
if (length(multiomics.list[[1]]) > 0 & !drop.miRNA) {
if (!full.search) { # Search only among the 198 genes in ACC, recommended
targets= get_multimir(mirna = multiomics.list[[1]],
target = gene.names,
table = table,
summary = T)
mRSG.target.genes = unique(targets@data$target_symbol)
} else { # Search the full dataset, not recommended.
# Use only if ACC gene search returns nothing or fails.
# Genes not in the ACC genes need to be manually removed.
targets= get_multimir(mirna = multiomics.list[[1]],
table = table,
summary = T)
mRSG.target.genes = unique(targets@data$target_symbol)
}
} else {
mRSG.target.genes = list()
}
#Remove suffix for Pathway Analysis Compatibility
R2Gn.genes = str_remove(multiomics.list[[2]], ".R2Gn")
RPPA.genes = str_remove(multiomics.list[[3]], ".RPPA")
#Join all cleaned-up genes are remove duplicates.
out1 = c(mRSG.target.genes, R2Gn.genes, RPPA.genes)
out = as.character(unique(out1))
out
}geneNames <- list("3F_0.5_Multi"=multiomics.to.GENES(names(sel.features$fold3$elasticnet_0.5$multigroup)),
"3F_0.5_One"=multiomics.to.GENES(names(sel.features$fold3$elasticnet_0.5$onegroup)),
"3F_1_Multi"=multiomics.to.GENES(names(sel.features$fold3$lasso$multigroup)),
"3F_1_One"=multiomics.to.GENES(names(sel.features$fold3$lasso$multigroup)),
# 5-Fold and 10-Fold CV results are exactly the same as 3-Fold,
# They are kept here for completeness.
"5F_0.5_Multi"=multiomics.to.GENES(names(sel.features$fold5$elasticnet_0.5$multigroup)),
"5F_0.5_One"=multiomics.to.GENES(names(sel.features$fold5$elasticnet_0.5$onegroup)),
"5F_1_Multi"=multiomics.to.GENES(names(sel.features$fold5$lasso$multigroup)),
"5F_1_One"=multiomics.to.GENES(names(sel.features$fold5$lasso$multigroup)),
"10F_0.5_Multi"=multiomics.to.GENES(names(sel.features$fold10$elasticnet_0.5$multigroup)),
"10F_0.5_One"=multiomics.to.GENES(names(sel.features$fold10$elasticnet_0.5$onegroup)),
"10F_1_Multi"=multiomics.to.GENES(names(sel.features$fold10$lasso$multigroup)),
"10F_1_One"=multiomics.to.GENES(names(sel.features$fold10$lasso$multigroup))
)geneNames## $`3F_0.5_Multi`
## [1] "FN1" "G6PD" "FASN" "MSH6" "TFRC"
##
## $`3F_0.5_One`
## [1] "FN1" "G6PD" "FASN" "PDCD4" "MSH6" "TFRC"
##
## $`3F_1_Multi`
## [1] "FN1" "G6PD" "FASN" "TFRC"
##
## $`3F_1_One`
## [1] "FN1" "G6PD" "FASN" "TFRC"
##
## $`5F_0.5_Multi`
## [1] "FN1" "G6PD" "FASN" "MSH6" "TFRC"
##
## $`5F_0.5_One`
## [1] "FN1" "G6PD" "FASN" "PDCD4" "MSH6" "TFRC"
##
## $`5F_1_Multi`
## [1] "FN1" "G6PD" "FASN" "TFRC"
##
## $`5F_1_One`
## [1] "FN1" "G6PD" "FASN" "TFRC"
##
## $`10F_0.5_Multi`
## [1] "FN1" "G6PD" "FASN" "MSH6" "TFRC"
##
## $`10F_0.5_One`
## [1] "FN1" "G6PD" "FASN" "PDCD4" "MSH6" "TFRC"
##
## $`10F_1_Multi`
## [1] "FN1" "G6PD" "FASN" "TFRC"
##
## $`10F_1_One`
## [1] "FN1" "G6PD" "FASN" "TFRC"saveRDS(geneNames, file = "data/sel_features/gene_converted/genes_squeezy.rds")2. Pathway Analysis
A. GO Classification
groupGO does not work with Squeey results, as there are too few genes (<=6) selected.
ggo_MF <- list()#functional profile of a geneset for Molecular Function
ggo_BP <- list()#functional profile of a geneset for Biological Process
ggo_CC <- list()#functional profile of a geneset for Cellular Component
for(z in 1:length(geneNames)){
print(z)
input <- geneNames[[z]]
ggo_MF[[z]] <- groupGO(gene=input,
OrgDb = org.Hs.eg.db,
ont="MF",
keyType="SYMBOL",
readable=TRUE)
ggo_BP[[z]] <- groupGO(gene=input,
OrgDb = org.Hs.eg.db,
ont="BP",
keyType="SYMBOL",
readable=TRUE)
ggo_CC[[z]] <- groupGO(gene=input,
OrgDb = org.Hs.eg.db,
ont="CC",
keyType="SYMBOL",
readable=TRUE)
}## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## [1] 11
## [1] 12for(z in 1:length(geneNames)) {
print(head(ggo_MF[[z]]))
print(head(ggo_BP[[z]]))
print(head(ggo_CC[[z]]))
}## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/5
## GO:0003824 GO:0003824 catalytic activity 3 3/5
## GO:0005198 GO:0005198 structural molecule activity 1 1/5
## GO:0005215 GO:0005215 transporter activity 0 0/5
## GO:0005488 GO:0005488 binding 5 5/5
## GO:0009055 GO:0009055 electron transfer activity 0 0/5
## geneID
## GO:0003774
## GO:0003824 G6PD/FASN/MSH6
## GO:0005198 FN1
## GO:0005215
## GO:0005488 FN1/G6PD/FASN/MSH6/TFRC
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 1 1/5
## GO:0002376 GO:0002376 immune system process 4 4/5
## GO:0008152 GO:0008152 metabolic process 5 5/5
## GO:0009987 GO:0009987 cellular process 5 5/5
## GO:0016032 GO:0016032 viral process 1 1/5
## GO:0022414 GO:0022414 reproductive process 1 1/5
## geneID
## GO:0000003 MSH6
## GO:0002376 FN1/G6PD/MSH6/TFRC
## GO:0008152 FN1/G6PD/FASN/MSH6/TFRC
## GO:0009987 FN1/G6PD/FASN/MSH6/TFRC
## GO:0016032 TFRC
## GO:0022414 MSH6
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 3 3/5
## GO:0044423 GO:0044423 virion component 0 0/5
## GO:0110165 GO:0110165 cellular anatomical entity 5 5/5
## geneID
## GO:0032991 FN1/MSH6/TFRC
## GO:0044423
## GO:0110165 FN1/G6PD/FASN/MSH6/TFRC
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/6
## GO:0003824 GO:0003824 catalytic activity 3 3/6
## GO:0005198 GO:0005198 structural molecule activity 1 1/6
## GO:0005215 GO:0005215 transporter activity 0 0/6
## GO:0005488 GO:0005488 binding 6 6/6
## GO:0009055 GO:0009055 electron transfer activity 0 0/6
## geneID
## GO:0003774
## GO:0003824 G6PD/FASN/MSH6
## GO:0005198 FN1
## GO:0005215
## GO:0005488 FN1/G6PD/FASN/PDCD4/MSH6/TFRC
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 1 1/6
## GO:0002376 GO:0002376 immune system process 4 4/6
## GO:0008152 GO:0008152 metabolic process 6 6/6
## GO:0009987 GO:0009987 cellular process 6 6/6
## GO:0016032 GO:0016032 viral process 1 1/6
## GO:0022414 GO:0022414 reproductive process 1 1/6
## geneID
## GO:0000003 MSH6
## GO:0002376 FN1/G6PD/MSH6/TFRC
## GO:0008152 FN1/G6PD/FASN/PDCD4/MSH6/TFRC
## GO:0009987 FN1/G6PD/FASN/PDCD4/MSH6/TFRC
## GO:0016032 TFRC
## GO:0022414 MSH6
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 3 3/6
## GO:0044423 GO:0044423 virion component 0 0/6
## GO:0110165 GO:0110165 cellular anatomical entity 6 6/6
## geneID
## GO:0032991 FN1/MSH6/TFRC
## GO:0044423
## GO:0110165 FN1/G6PD/FASN/PDCD4/MSH6/TFRC
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/4
## GO:0003824 GO:0003824 catalytic activity 2 2/4
## GO:0005198 GO:0005198 structural molecule activity 1 1/4
## GO:0005215 GO:0005215 transporter activity 0 0/4
## GO:0005488 GO:0005488 binding 4 4/4
## GO:0009055 GO:0009055 electron transfer activity 0 0/4
## geneID
## GO:0003774
## GO:0003824 G6PD/FASN
## GO:0005198 FN1
## GO:0005215
## GO:0005488 FN1/G6PD/FASN/TFRC
## GO:0009055
## ID Description Count GeneRatio geneID
## GO:0000003 GO:0000003 reproduction 0 0/4
## GO:0002376 GO:0002376 immune system process 3 3/4 FN1/G6PD/TFRC
## GO:0008152 GO:0008152 metabolic process 4 4/4 FN1/G6PD/FASN/TFRC
## GO:0009987 GO:0009987 cellular process 4 4/4 FN1/G6PD/FASN/TFRC
## GO:0016032 GO:0016032 viral process 1 1/4 TFRC
## GO:0022414 GO:0022414 reproductive process 0 0/4
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 2 2/4
## GO:0044423 GO:0044423 virion component 0 0/4
## GO:0110165 GO:0110165 cellular anatomical entity 4 4/4
## geneID
## GO:0032991 FN1/TFRC
## GO:0044423
## GO:0110165 FN1/G6PD/FASN/TFRC
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/4
## GO:0003824 GO:0003824 catalytic activity 2 2/4
## GO:0005198 GO:0005198 structural molecule activity 1 1/4
## GO:0005215 GO:0005215 transporter activity 0 0/4
## GO:0005488 GO:0005488 binding 4 4/4
## GO:0009055 GO:0009055 electron transfer activity 0 0/4
## geneID
## GO:0003774
## GO:0003824 G6PD/FASN
## GO:0005198 FN1
## GO:0005215
## GO:0005488 FN1/G6PD/FASN/TFRC
## GO:0009055
## ID Description Count GeneRatio geneID
## GO:0000003 GO:0000003 reproduction 0 0/4
## GO:0002376 GO:0002376 immune system process 3 3/4 FN1/G6PD/TFRC
## GO:0008152 GO:0008152 metabolic process 4 4/4 FN1/G6PD/FASN/TFRC
## GO:0009987 GO:0009987 cellular process 4 4/4 FN1/G6PD/FASN/TFRC
## GO:0016032 GO:0016032 viral process 1 1/4 TFRC
## GO:0022414 GO:0022414 reproductive process 0 0/4
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 2 2/4
## GO:0044423 GO:0044423 virion component 0 0/4
## GO:0110165 GO:0110165 cellular anatomical entity 4 4/4
## geneID
## GO:0032991 FN1/TFRC
## GO:0044423
## GO:0110165 FN1/G6PD/FASN/TFRC
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/5
## GO:0003824 GO:0003824 catalytic activity 3 3/5
## GO:0005198 GO:0005198 structural molecule activity 1 1/5
## GO:0005215 GO:0005215 transporter activity 0 0/5
## GO:0005488 GO:0005488 binding 5 5/5
## GO:0009055 GO:0009055 electron transfer activity 0 0/5
## geneID
## GO:0003774
## GO:0003824 G6PD/FASN/MSH6
## GO:0005198 FN1
## GO:0005215
## GO:0005488 FN1/G6PD/FASN/MSH6/TFRC
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 1 1/5
## GO:0002376 GO:0002376 immune system process 4 4/5
## GO:0008152 GO:0008152 metabolic process 5 5/5
## GO:0009987 GO:0009987 cellular process 5 5/5
## GO:0016032 GO:0016032 viral process 1 1/5
## GO:0022414 GO:0022414 reproductive process 1 1/5
## geneID
## GO:0000003 MSH6
## GO:0002376 FN1/G6PD/MSH6/TFRC
## GO:0008152 FN1/G6PD/FASN/MSH6/TFRC
## GO:0009987 FN1/G6PD/FASN/MSH6/TFRC
## GO:0016032 TFRC
## GO:0022414 MSH6
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 3 3/5
## GO:0044423 GO:0044423 virion component 0 0/5
## GO:0110165 GO:0110165 cellular anatomical entity 5 5/5
## geneID
## GO:0032991 FN1/MSH6/TFRC
## GO:0044423
## GO:0110165 FN1/G6PD/FASN/MSH6/TFRC
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/6
## GO:0003824 GO:0003824 catalytic activity 3 3/6
## GO:0005198 GO:0005198 structural molecule activity 1 1/6
## GO:0005215 GO:0005215 transporter activity 0 0/6
## GO:0005488 GO:0005488 binding 6 6/6
## GO:0009055 GO:0009055 electron transfer activity 0 0/6
## geneID
## GO:0003774
## GO:0003824 G6PD/FASN/MSH6
## GO:0005198 FN1
## GO:0005215
## GO:0005488 FN1/G6PD/FASN/PDCD4/MSH6/TFRC
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 1 1/6
## GO:0002376 GO:0002376 immune system process 4 4/6
## GO:0008152 GO:0008152 metabolic process 6 6/6
## GO:0009987 GO:0009987 cellular process 6 6/6
## GO:0016032 GO:0016032 viral process 1 1/6
## GO:0022414 GO:0022414 reproductive process 1 1/6
## geneID
## GO:0000003 MSH6
## GO:0002376 FN1/G6PD/MSH6/TFRC
## GO:0008152 FN1/G6PD/FASN/PDCD4/MSH6/TFRC
## GO:0009987 FN1/G6PD/FASN/PDCD4/MSH6/TFRC
## GO:0016032 TFRC
## GO:0022414 MSH6
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 3 3/6
## GO:0044423 GO:0044423 virion component 0 0/6
## GO:0110165 GO:0110165 cellular anatomical entity 6 6/6
## geneID
## GO:0032991 FN1/MSH6/TFRC
## GO:0044423
## GO:0110165 FN1/G6PD/FASN/PDCD4/MSH6/TFRC
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/4
## GO:0003824 GO:0003824 catalytic activity 2 2/4
## GO:0005198 GO:0005198 structural molecule activity 1 1/4
## GO:0005215 GO:0005215 transporter activity 0 0/4
## GO:0005488 GO:0005488 binding 4 4/4
## GO:0009055 GO:0009055 electron transfer activity 0 0/4
## geneID
## GO:0003774
## GO:0003824 G6PD/FASN
## GO:0005198 FN1
## GO:0005215
## GO:0005488 FN1/G6PD/FASN/TFRC
## GO:0009055
## ID Description Count GeneRatio geneID
## GO:0000003 GO:0000003 reproduction 0 0/4
## GO:0002376 GO:0002376 immune system process 3 3/4 FN1/G6PD/TFRC
## GO:0008152 GO:0008152 metabolic process 4 4/4 FN1/G6PD/FASN/TFRC
## GO:0009987 GO:0009987 cellular process 4 4/4 FN1/G6PD/FASN/TFRC
## GO:0016032 GO:0016032 viral process 1 1/4 TFRC
## GO:0022414 GO:0022414 reproductive process 0 0/4
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 2 2/4
## GO:0044423 GO:0044423 virion component 0 0/4
## GO:0110165 GO:0110165 cellular anatomical entity 4 4/4
## geneID
## GO:0032991 FN1/TFRC
## GO:0044423
## GO:0110165 FN1/G6PD/FASN/TFRC
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/4
## GO:0003824 GO:0003824 catalytic activity 2 2/4
## GO:0005198 GO:0005198 structural molecule activity 1 1/4
## GO:0005215 GO:0005215 transporter activity 0 0/4
## GO:0005488 GO:0005488 binding 4 4/4
## GO:0009055 GO:0009055 electron transfer activity 0 0/4
## geneID
## GO:0003774
## GO:0003824 G6PD/FASN
## GO:0005198 FN1
## GO:0005215
## GO:0005488 FN1/G6PD/FASN/TFRC
## GO:0009055
## ID Description Count GeneRatio geneID
## GO:0000003 GO:0000003 reproduction 0 0/4
## GO:0002376 GO:0002376 immune system process 3 3/4 FN1/G6PD/TFRC
## GO:0008152 GO:0008152 metabolic process 4 4/4 FN1/G6PD/FASN/TFRC
## GO:0009987 GO:0009987 cellular process 4 4/4 FN1/G6PD/FASN/TFRC
## GO:0016032 GO:0016032 viral process 1 1/4 TFRC
## GO:0022414 GO:0022414 reproductive process 0 0/4
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 2 2/4
## GO:0044423 GO:0044423 virion component 0 0/4
## GO:0110165 GO:0110165 cellular anatomical entity 4 4/4
## geneID
## GO:0032991 FN1/TFRC
## GO:0044423
## GO:0110165 FN1/G6PD/FASN/TFRC
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/5
## GO:0003824 GO:0003824 catalytic activity 3 3/5
## GO:0005198 GO:0005198 structural molecule activity 1 1/5
## GO:0005215 GO:0005215 transporter activity 0 0/5
## GO:0005488 GO:0005488 binding 5 5/5
## GO:0009055 GO:0009055 electron transfer activity 0 0/5
## geneID
## GO:0003774
## GO:0003824 G6PD/FASN/MSH6
## GO:0005198 FN1
## GO:0005215
## GO:0005488 FN1/G6PD/FASN/MSH6/TFRC
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 1 1/5
## GO:0002376 GO:0002376 immune system process 4 4/5
## GO:0008152 GO:0008152 metabolic process 5 5/5
## GO:0009987 GO:0009987 cellular process 5 5/5
## GO:0016032 GO:0016032 viral process 1 1/5
## GO:0022414 GO:0022414 reproductive process 1 1/5
## geneID
## GO:0000003 MSH6
## GO:0002376 FN1/G6PD/MSH6/TFRC
## GO:0008152 FN1/G6PD/FASN/MSH6/TFRC
## GO:0009987 FN1/G6PD/FASN/MSH6/TFRC
## GO:0016032 TFRC
## GO:0022414 MSH6
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 3 3/5
## GO:0044423 GO:0044423 virion component 0 0/5
## GO:0110165 GO:0110165 cellular anatomical entity 5 5/5
## geneID
## GO:0032991 FN1/MSH6/TFRC
## GO:0044423
## GO:0110165 FN1/G6PD/FASN/MSH6/TFRC
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/6
## GO:0003824 GO:0003824 catalytic activity 3 3/6
## GO:0005198 GO:0005198 structural molecule activity 1 1/6
## GO:0005215 GO:0005215 transporter activity 0 0/6
## GO:0005488 GO:0005488 binding 6 6/6
## GO:0009055 GO:0009055 electron transfer activity 0 0/6
## geneID
## GO:0003774
## GO:0003824 G6PD/FASN/MSH6
## GO:0005198 FN1
## GO:0005215
## GO:0005488 FN1/G6PD/FASN/PDCD4/MSH6/TFRC
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 1 1/6
## GO:0002376 GO:0002376 immune system process 4 4/6
## GO:0008152 GO:0008152 metabolic process 6 6/6
## GO:0009987 GO:0009987 cellular process 6 6/6
## GO:0016032 GO:0016032 viral process 1 1/6
## GO:0022414 GO:0022414 reproductive process 1 1/6
## geneID
## GO:0000003 MSH6
## GO:0002376 FN1/G6PD/MSH6/TFRC
## GO:0008152 FN1/G6PD/FASN/PDCD4/MSH6/TFRC
## GO:0009987 FN1/G6PD/FASN/PDCD4/MSH6/TFRC
## GO:0016032 TFRC
## GO:0022414 MSH6
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 3 3/6
## GO:0044423 GO:0044423 virion component 0 0/6
## GO:0110165 GO:0110165 cellular anatomical entity 6 6/6
## geneID
## GO:0032991 FN1/MSH6/TFRC
## GO:0044423
## GO:0110165 FN1/G6PD/FASN/PDCD4/MSH6/TFRC
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/4
## GO:0003824 GO:0003824 catalytic activity 2 2/4
## GO:0005198 GO:0005198 structural molecule activity 1 1/4
## GO:0005215 GO:0005215 transporter activity 0 0/4
## GO:0005488 GO:0005488 binding 4 4/4
## GO:0009055 GO:0009055 electron transfer activity 0 0/4
## geneID
## GO:0003774
## GO:0003824 G6PD/FASN
## GO:0005198 FN1
## GO:0005215
## GO:0005488 FN1/G6PD/FASN/TFRC
## GO:0009055
## ID Description Count GeneRatio geneID
## GO:0000003 GO:0000003 reproduction 0 0/4
## GO:0002376 GO:0002376 immune system process 3 3/4 FN1/G6PD/TFRC
## GO:0008152 GO:0008152 metabolic process 4 4/4 FN1/G6PD/FASN/TFRC
## GO:0009987 GO:0009987 cellular process 4 4/4 FN1/G6PD/FASN/TFRC
## GO:0016032 GO:0016032 viral process 1 1/4 TFRC
## GO:0022414 GO:0022414 reproductive process 0 0/4
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 2 2/4
## GO:0044423 GO:0044423 virion component 0 0/4
## GO:0110165 GO:0110165 cellular anatomical entity 4 4/4
## geneID
## GO:0032991 FN1/TFRC
## GO:0044423
## GO:0110165 FN1/G6PD/FASN/TFRC
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/4
## GO:0003824 GO:0003824 catalytic activity 2 2/4
## GO:0005198 GO:0005198 structural molecule activity 1 1/4
## GO:0005215 GO:0005215 transporter activity 0 0/4
## GO:0005488 GO:0005488 binding 4 4/4
## GO:0009055 GO:0009055 electron transfer activity 0 0/4
## geneID
## GO:0003774
## GO:0003824 G6PD/FASN
## GO:0005198 FN1
## GO:0005215
## GO:0005488 FN1/G6PD/FASN/TFRC
## GO:0009055
## ID Description Count GeneRatio geneID
## GO:0000003 GO:0000003 reproduction 0 0/4
## GO:0002376 GO:0002376 immune system process 3 3/4 FN1/G6PD/TFRC
## GO:0008152 GO:0008152 metabolic process 4 4/4 FN1/G6PD/FASN/TFRC
## GO:0009987 GO:0009987 cellular process 4 4/4 FN1/G6PD/FASN/TFRC
## GO:0016032 GO:0016032 viral process 1 1/4 TFRC
## GO:0022414 GO:0022414 reproductive process 0 0/4
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 2 2/4
## GO:0044423 GO:0044423 virion component 0 0/4
## GO:0110165 GO:0110165 cellular anatomical entity 4 4/4
## geneID
## GO:0032991 FN1/TFRC
## GO:0044423
## GO:0110165 FN1/G6PD/FASN/TFRCbarplot(ggo_MF[[1]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, Multigroup")
barplot(ggo_MF[[2]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, Onegroup")
barplot(ggo_MF[[3]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 1, Multigroup")
barplot(ggo_MF[[4]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 1, Multigroup")
barplot(ggo_MF[[5]], title = "groupGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, Multigroup")
barplot(ggo_MF[[6]], title = "groupGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, Onegroup")
barplot(ggo_MF[[7]], title = "groupGO, Molecular Function, \n 5-Fold CV, alpha = 1, Multigroup")
barplot(ggo_MF[[8]], title = "groupGO, Molecular Function, \n 5-Fold CV, alpha = 1, Onegroup")
barplot(ggo_MF[[9]], title = "groupGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Multigroup")
barplot(ggo_MF[[10]], title = "groupGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Onegroup")
barplot(ggo_MF[[11]], title = "groupGO, Molecular Function, \n 10-Fold CV, alpha = 1, Multigroup")
barplot(ggo_MF[[12]], title = "groupGO, Molecular Function, \n 10-Fold CV, alpha = 1, Onegroup")
barplot(ggo_BP[[1]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 0.5, Multigroup")
barplot(ggo_BP[[2]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 0.5, Onegroup")
barplot(ggo_BP[[3]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 1, Multigroup")
barplot(ggo_BP[[4]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 1, Multigroup")
barplot(ggo_BP[[5]], title = "groupGO, Biological Process, \n 5-Fold CV, alpha = 0.5, Multigroup")
barplot(ggo_BP[[6]], title = "groupGO, Biological Process, \n 5-Fold CV, alpha = 0.5, Onegroup")
barplot(ggo_BP[[7]], title = "groupGO, Biological Process, \n 5-Fold CV, alpha = 1, Multigroup")
barplot(ggo_BP[[8]], title = "groupGO, Biological Process, \n 5-Fold CV, alpha = 1, Onegroup")
barplot(ggo_BP[[9]], title = "groupGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Multigroup")
barplot(ggo_BP[[10]], title = "groupGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Onegroup")
barplot(ggo_BP[[11]], title = "groupGO, Biological Process, \n 10-Fold CV, alpha = 1, Multigroup")
barplot(ggo_BP[[12]], title = "groupGO, Biological Process, \n 10-Fold CV, alpha = 1, Onegroup")
barplot(ggo_CC[[1]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, Multigroup")
barplot(ggo_CC[[2]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, Onegroup")
barplot(ggo_CC[[3]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 1, Multigroup")
barplot(ggo_CC[[4]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 1, Multigroup")
barplot(ggo_CC[[5]], title = "groupGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, Multigroup")
barplot(ggo_CC[[6]], title = "groupGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, Onegroup")
barplot(ggo_CC[[7]], title = "groupGO, Cellular Component, \n 5-Fold CV, alpha = 1, Multigroup")
barplot(ggo_CC[[8]], title = "groupGO, Cellular Component, \n 5-Fold CV, alpha = 1, Onegroup")
barplot(ggo_CC[[9]], title = "groupGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Multigroup")
barplot(ggo_CC[[10]], title = "groupGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Onegroup")
barplot(ggo_CC[[11]], title = "groupGO, Cellular Component, \n 10-Fold CV, alpha = 1, Multigroup")
barplot(ggo_CC[[12]], title = "groupGO, Cellular Component, \n 10-Fold CV, alpha = 1, Onegroup")
B. GO Over-Representation
ego_MF <- list()#GO enrichment of a geneset for Molecular Function
ego_BP <- list()#GO enrichment of a geneset for Biological Process
ego_CC <- list()#GO enrichment of a geneset for Cellular Component
for(z in 1:length(geneNames)){
print(z)
input <- geneNames[[z]]
ego_MF[[z]] <- enrichGO(
gene = input,
OrgDb = org.Hs.eg.db,
ont = "MF",
pAdjustMethod = "BH",
keyType="SYMBOL",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
minGSSize = 2,
readable = TRUE)
ego_BP[[z]] <- enrichGO(
gene = input,
OrgDb = org.Hs.eg.db,
ont = "BP",
pAdjustMethod = "BH",
keyType="SYMBOL",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
minGSSize = 2,
readable = TRUE)
ego_CC[[z]] <- enrichGO(
gene = input,
OrgDb = org.Hs.eg.db,
ont = "CC",
pAdjustMethod = "BH",
keyType="SYMBOL",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
minGSSize = 2,
readable = TRUE)
}## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## [1] 11
## [1] 12for(z in 1:length(geneNames)){
print(head(ego_MF[[z]]))
print(head(ego_BP[[z]]))
print(head(ego_CC[[z]]))
}## ID
## GO:0016616 GO:0016616
## GO:0016614 GO:0016614
## GO:0004314 GO:0004314
## GO:0004315 GO:0004315
## GO:0004316 GO:0004316
## GO:0004345 GO:0004345
## Description
## GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
## GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
## GO:0004314 [acyl-carrier-protein] S-malonyltransferase activity
## GO:0004315 3-oxoacyl-[acyl-carrier-protein] synthase activity
## GO:0004316 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
## GO:0004345 glucose-6-phosphate dehydrogenase activity
## GeneRatio BgRatio pvalue p.adjust qvalue geneID
## GO:0016616 2/5 125/18522 0.0004458624 0.002463021 0.0003906738 G6PD/FASN
## GO:0016614 2/5 135/18522 0.0005198010 0.002463021 0.0003906738 G6PD/FASN
## GO:0004314 1/5 2/18522 0.0005398402 0.002463021 0.0003906738 FASN
## GO:0004315 1/5 2/18522 0.0005398402 0.002463021 0.0003906738 FASN
## GO:0004316 1/5 2/18522 0.0005398402 0.002463021 0.0003906738 FASN
## GO:0004345 1/5 2/18522 0.0005398402 0.002463021 0.0003906738 G6PD
## Count
## GO:0016616 2
## GO:0016614 2
## GO:0004314 1
## GO:0004315 1
## GO:0004316 1
## GO:0004345 1
## ID
## GO:0010039 GO:0010039
## GO:0044403 GO:0044403
## GO:0006953 GO:0006953
## GO:0002204 GO:0002204
## GO:0002208 GO:0002208
## GO:0045190 GO:0045190
## Description
## GO:0010039 response to iron ion
## GO:0044403 biological process involved in symbiotic interaction
## GO:0006953 acute-phase response
## GO:0002204 somatic recombination of immunoglobulin genes involved in immune response
## GO:0002208 somatic diversification of immunoglobulins involved in immune response
## GO:0045190 isotype switching
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0010039 2/5 28/18888 2.113375e-05 0.00436869 0.001521082
## GO:0044403 3/5 311/18888 4.314255e-05 0.00436869 0.001521082
## GO:0006953 2/5 47/18888 6.031646e-05 0.00436869 0.001521082
## GO:0002204 2/5 53/18888 7.683924e-05 0.00436869 0.001521082
## GO:0002208 2/5 53/18888 7.683924e-05 0.00436869 0.001521082
## GO:0045190 2/5 53/18888 7.683924e-05 0.00436869 0.001521082
## geneID Count
## GO:0010039 G6PD/TFRC 2
## GO:0044403 FN1/FASN/TFRC 3
## GO:0006953 FN1/TFRC 2
## GO:0002204 MSH6/TFRC 2
## GO:0002208 MSH6/TFRC 2
## GO:0045190 MSH6/TFRC 2
## ID Description GeneRatio BgRatio pvalue
## GO:0042470 GO:0042470 melanosome 2/5 112/19894 0.0003106766
## GO:0048770 GO:0048770 pigment granule 2/5 112/19894 0.0003106766
## GO:0032301 GO:0032301 MutSalpha complex 1/5 2/19894 0.0005026136
## GO:0072562 GO:0072562 blood microparticle 2/5 144/19894 0.0005129374
## GO:0042587 GO:0042587 glycogen granule 1/5 6/19894 0.0015072345
## GO:0005577 GO:0005577 fibrinogen complex 1/5 8/19894 0.0020092419
## p.adjust qvalue geneID Count
## GO:0042470 0.00500114 0.002564687 FASN/TFRC 2
## GO:0048770 0.00500114 0.002564687 FASN/TFRC 2
## GO:0032301 0.00500114 0.002564687 MSH6 1
## GO:0072562 0.00500114 0.002564687 FN1/TFRC 2
## GO:0042587 0.01119435 0.005740691 FASN 1
## GO:0005577 0.01119435 0.005740691 FN1 1
## ID
## GO:0004314 GO:0004314
## GO:0004315 GO:0004315
## GO:0004316 GO:0004316
## GO:0004345 GO:0004345
## GO:0004998 GO:0004998
## GO:0008659 GO:0008659
## Description
## GO:0004314 [acyl-carrier-protein] S-malonyltransferase activity
## GO:0004315 3-oxoacyl-[acyl-carrier-protein] synthase activity
## GO:0004316 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
## GO:0004345 glucose-6-phosphate dehydrogenase activity
## GO:0004998 transferrin receptor activity
## GO:0008659 (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity
## GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
## GO:0004314 1/6 2/18522 0.0006477907 0.003240407 0.0006541557 FASN 1
## GO:0004315 1/6 2/18522 0.0006477907 0.003240407 0.0006541557 FASN 1
## GO:0004316 1/6 2/18522 0.0006477907 0.003240407 0.0006541557 FASN 1
## GO:0004345 1/6 2/18522 0.0006477907 0.003240407 0.0006541557 G6PD 1
## GO:0004998 1/6 2/18522 0.0006477907 0.003240407 0.0006541557 TFRC 1
## GO:0008659 1/6 2/18522 0.0006477907 0.003240407 0.0006541557 FASN 1
## ID
## GO:0010039 GO:0010039
## GO:0044403 GO:0044403
## GO:0006953 GO:0006953
## GO:0002204 GO:0002204
## GO:0002208 GO:0002208
## GO:0045190 GO:0045190
## Description
## GO:0010039 response to iron ion
## GO:0044403 biological process involved in symbiotic interaction
## GO:0006953 acute-phase response
## GO:0002204 somatic recombination of immunoglobulin genes involved in immune response
## GO:0002208 somatic diversification of immunoglobulins involved in immune response
## GO:0045190 isotype switching
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0010039 2/6 28/18888 3.167154e-05 0.00792854 0.003156436
## GO:0044403 3/6 311/18888 8.523132e-05 0.00792854 0.003156436
## GO:0006953 2/6 47/18888 9.033104e-05 0.00792854 0.003156436
## GO:0002204 2/6 53/18888 1.150515e-04 0.00792854 0.003156436
## GO:0002208 2/6 53/18888 1.150515e-04 0.00792854 0.003156436
## GO:0045190 2/6 53/18888 1.150515e-04 0.00792854 0.003156436
## geneID Count
## GO:0010039 G6PD/TFRC 2
## GO:0044403 FN1/FASN/TFRC 3
## GO:0006953 FN1/TFRC 2
## GO:0002204 MSH6/TFRC 2
## GO:0002208 MSH6/TFRC 2
## GO:0045190 MSH6/TFRC 2
## ID Description GeneRatio BgRatio pvalue
## GO:0042470 GO:0042470 melanosome 2/6 112/19894 0.0004642992
## GO:0048770 GO:0048770 pigment granule 2/6 112/19894 0.0004642992
## GO:0032301 GO:0032301 MutSalpha complex 1/6 2/19894 0.0006031211
## GO:0072562 GO:0072562 blood microparticle 2/6 144/19894 0.0007657506
## GO:0042587 GO:0042587 glycogen granule 1/6 6/19894 0.0018084541
## GO:0005577 GO:0005577 fibrinogen complex 1/6 8/19894 0.0024106661
## p.adjust qvalue geneID Count
## GO:0042470 0.007466069 0.004030266 FASN/TFRC 2
## GO:0048770 0.007466069 0.004030266 FASN/TFRC 2
## GO:0032301 0.007466069 0.004030266 MSH6 1
## GO:0072562 0.007466069 0.004030266 FN1/TFRC 2
## GO:0042587 0.013430854 0.007250124 FASN 1
## GO:0005577 0.013430854 0.007250124 FN1 1
## ID
## GO:0016616 GO:0016616
## GO:0016614 GO:0016614
## GO:0004314 GO:0004314
## GO:0004315 GO:0004315
## GO:0004316 GO:0004316
## GO:0004345 GO:0004345
## Description
## GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
## GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
## GO:0004314 [acyl-carrier-protein] S-malonyltransferase activity
## GO:0004315 3-oxoacyl-[acyl-carrier-protein] synthase activity
## GO:0004316 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
## GO:0004345 glucose-6-phosphate dehydrogenase activity
## GeneRatio BgRatio pvalue p.adjust qvalue geneID
## GO:0016616 2/4 125/18522 0.0002687060 0.00141082 0.0001515382 G6PD/FASN
## GO:0016614 2/4 135/18522 0.0003133792 0.00141082 0.0001515382 G6PD/FASN
## GO:0004314 1/4 2/18522 0.0004318838 0.00141082 0.0001515382 FASN
## GO:0004315 1/4 2/18522 0.0004318838 0.00141082 0.0001515382 FASN
## GO:0004316 1/4 2/18522 0.0004318838 0.00141082 0.0001515382 FASN
## GO:0004345 1/4 2/18522 0.0004318838 0.00141082 0.0001515382 G6PD
## Count
## GO:0016616 2
## GO:0016614 2
## GO:0004314 1
## GO:0004315 1
## GO:0004316 1
## GO:0004345 1
## ID Description
## GO:0010039 GO:0010039 response to iron ion
## GO:0044403 GO:0044403 biological process involved in symbiotic interaction
## GO:0006953 GO:0006953 acute-phase response
## GO:0030099 GO:0030099 myeloid cell differentiation
## GO:0002526 GO:0002526 acute inflammatory response
## GO:0051702 GO:0051702 biological process involved in interaction with symbiont
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0010039 2/4 28/18888 1.269190e-05 0.003249522 0.001020648
## GO:0044403 3/4 311/18888 1.747055e-05 0.003249522 0.001020648
## GO:0006953 2/4 47/18888 3.624743e-05 0.004494682 0.001411742
## GO:0030099 3/4 439/18888 4.902361e-05 0.004559196 0.001432005
## GO:0002526 2/4 109/18888 1.965017e-04 0.013128987 0.004123706
## GO:0051702 2/4 119/18888 2.342272e-04 0.013128987 0.004123706
## geneID Count
## GO:0010039 G6PD/TFRC 2
## GO:0044403 FN1/FASN/TFRC 3
## GO:0006953 FN1/TFRC 2
## GO:0030099 G6PD/FASN/TFRC 3
## GO:0002526 FN1/TFRC 2
## GO:0051702 FN1/FASN 2
## ID Description GeneRatio BgRatio
## GO:0042470 GO:0042470 melanosome 2/4 112/19894
## GO:0048770 GO:0048770 pigment granule 2/4 112/19894
## GO:0072562 GO:0072562 blood microparticle 2/4 144/19894
## GO:0042587 GO:0042587 glycogen granule 1/4 6/19894
## GO:0005577 GO:0005577 fibrinogen complex 1/4 8/19894
## GO:1990712 GO:1990712 HFE-transferrin receptor complex 1/4 8/19894
## pvalue p.adjust qvalue geneID Count
## GO:0042470 0.0001870951 0.003461260 0.001477067 FASN/TFRC 2
## GO:0048770 0.0001870951 0.003461260 0.001477067 FASN/TFRC 2
## GO:0072562 0.0003092324 0.003813867 0.001627539 FN1/TFRC 2
## GO:0042587 0.0012059391 0.009914004 0.004230727 FASN 1
## GO:0005577 0.0016076763 0.009914004 0.004230727 FN1 1
## GO:1990712 0.0016076763 0.009914004 0.004230727 TFRC 1
## ID
## GO:0016616 GO:0016616
## GO:0016614 GO:0016614
## GO:0004314 GO:0004314
## GO:0004315 GO:0004315
## GO:0004316 GO:0004316
## GO:0004345 GO:0004345
## Description
## GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
## GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
## GO:0004314 [acyl-carrier-protein] S-malonyltransferase activity
## GO:0004315 3-oxoacyl-[acyl-carrier-protein] synthase activity
## GO:0004316 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
## GO:0004345 glucose-6-phosphate dehydrogenase activity
## GeneRatio BgRatio pvalue p.adjust qvalue geneID
## GO:0016616 2/4 125/18522 0.0002687060 0.00141082 0.0001515382 G6PD/FASN
## GO:0016614 2/4 135/18522 0.0003133792 0.00141082 0.0001515382 G6PD/FASN
## GO:0004314 1/4 2/18522 0.0004318838 0.00141082 0.0001515382 FASN
## GO:0004315 1/4 2/18522 0.0004318838 0.00141082 0.0001515382 FASN
## GO:0004316 1/4 2/18522 0.0004318838 0.00141082 0.0001515382 FASN
## GO:0004345 1/4 2/18522 0.0004318838 0.00141082 0.0001515382 G6PD
## Count
## GO:0016616 2
## GO:0016614 2
## GO:0004314 1
## GO:0004315 1
## GO:0004316 1
## GO:0004345 1
## ID Description
## GO:0010039 GO:0010039 response to iron ion
## GO:0044403 GO:0044403 biological process involved in symbiotic interaction
## GO:0006953 GO:0006953 acute-phase response
## GO:0030099 GO:0030099 myeloid cell differentiation
## GO:0002526 GO:0002526 acute inflammatory response
## GO:0051702 GO:0051702 biological process involved in interaction with symbiont
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0010039 2/4 28/18888 1.269190e-05 0.003249522 0.001020648
## GO:0044403 3/4 311/18888 1.747055e-05 0.003249522 0.001020648
## GO:0006953 2/4 47/18888 3.624743e-05 0.004494682 0.001411742
## GO:0030099 3/4 439/18888 4.902361e-05 0.004559196 0.001432005
## GO:0002526 2/4 109/18888 1.965017e-04 0.013128987 0.004123706
## GO:0051702 2/4 119/18888 2.342272e-04 0.013128987 0.004123706
## geneID Count
## GO:0010039 G6PD/TFRC 2
## GO:0044403 FN1/FASN/TFRC 3
## GO:0006953 FN1/TFRC 2
## GO:0030099 G6PD/FASN/TFRC 3
## GO:0002526 FN1/TFRC 2
## GO:0051702 FN1/FASN 2
## ID Description GeneRatio BgRatio
## GO:0042470 GO:0042470 melanosome 2/4 112/19894
## GO:0048770 GO:0048770 pigment granule 2/4 112/19894
## GO:0072562 GO:0072562 blood microparticle 2/4 144/19894
## GO:0042587 GO:0042587 glycogen granule 1/4 6/19894
## GO:0005577 GO:0005577 fibrinogen complex 1/4 8/19894
## GO:1990712 GO:1990712 HFE-transferrin receptor complex 1/4 8/19894
## pvalue p.adjust qvalue geneID Count
## GO:0042470 0.0001870951 0.003461260 0.001477067 FASN/TFRC 2
## GO:0048770 0.0001870951 0.003461260 0.001477067 FASN/TFRC 2
## GO:0072562 0.0003092324 0.003813867 0.001627539 FN1/TFRC 2
## GO:0042587 0.0012059391 0.009914004 0.004230727 FASN 1
## GO:0005577 0.0016076763 0.009914004 0.004230727 FN1 1
## GO:1990712 0.0016076763 0.009914004 0.004230727 TFRC 1
## ID
## GO:0016616 GO:0016616
## GO:0016614 GO:0016614
## GO:0004314 GO:0004314
## GO:0004315 GO:0004315
## GO:0004316 GO:0004316
## GO:0004345 GO:0004345
## Description
## GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
## GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
## GO:0004314 [acyl-carrier-protein] S-malonyltransferase activity
## GO:0004315 3-oxoacyl-[acyl-carrier-protein] synthase activity
## GO:0004316 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
## GO:0004345 glucose-6-phosphate dehydrogenase activity
## GeneRatio BgRatio pvalue p.adjust qvalue geneID
## GO:0016616 2/5 125/18522 0.0004458624 0.002463021 0.0003906738 G6PD/FASN
## GO:0016614 2/5 135/18522 0.0005198010 0.002463021 0.0003906738 G6PD/FASN
## GO:0004314 1/5 2/18522 0.0005398402 0.002463021 0.0003906738 FASN
## GO:0004315 1/5 2/18522 0.0005398402 0.002463021 0.0003906738 FASN
## GO:0004316 1/5 2/18522 0.0005398402 0.002463021 0.0003906738 FASN
## GO:0004345 1/5 2/18522 0.0005398402 0.002463021 0.0003906738 G6PD
## Count
## GO:0016616 2
## GO:0016614 2
## GO:0004314 1
## GO:0004315 1
## GO:0004316 1
## GO:0004345 1
## ID
## GO:0010039 GO:0010039
## GO:0044403 GO:0044403
## GO:0006953 GO:0006953
## GO:0002204 GO:0002204
## GO:0002208 GO:0002208
## GO:0045190 GO:0045190
## Description
## GO:0010039 response to iron ion
## GO:0044403 biological process involved in symbiotic interaction
## GO:0006953 acute-phase response
## GO:0002204 somatic recombination of immunoglobulin genes involved in immune response
## GO:0002208 somatic diversification of immunoglobulins involved in immune response
## GO:0045190 isotype switching
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0010039 2/5 28/18888 2.113375e-05 0.00436869 0.001521082
## GO:0044403 3/5 311/18888 4.314255e-05 0.00436869 0.001521082
## GO:0006953 2/5 47/18888 6.031646e-05 0.00436869 0.001521082
## GO:0002204 2/5 53/18888 7.683924e-05 0.00436869 0.001521082
## GO:0002208 2/5 53/18888 7.683924e-05 0.00436869 0.001521082
## GO:0045190 2/5 53/18888 7.683924e-05 0.00436869 0.001521082
## geneID Count
## GO:0010039 G6PD/TFRC 2
## GO:0044403 FN1/FASN/TFRC 3
## GO:0006953 FN1/TFRC 2
## GO:0002204 MSH6/TFRC 2
## GO:0002208 MSH6/TFRC 2
## GO:0045190 MSH6/TFRC 2
## ID Description GeneRatio BgRatio pvalue
## GO:0042470 GO:0042470 melanosome 2/5 112/19894 0.0003106766
## GO:0048770 GO:0048770 pigment granule 2/5 112/19894 0.0003106766
## GO:0032301 GO:0032301 MutSalpha complex 1/5 2/19894 0.0005026136
## GO:0072562 GO:0072562 blood microparticle 2/5 144/19894 0.0005129374
## GO:0042587 GO:0042587 glycogen granule 1/5 6/19894 0.0015072345
## GO:0005577 GO:0005577 fibrinogen complex 1/5 8/19894 0.0020092419
## p.adjust qvalue geneID Count
## GO:0042470 0.00500114 0.002564687 FASN/TFRC 2
## GO:0048770 0.00500114 0.002564687 FASN/TFRC 2
## GO:0032301 0.00500114 0.002564687 MSH6 1
## GO:0072562 0.00500114 0.002564687 FN1/TFRC 2
## GO:0042587 0.01119435 0.005740691 FASN 1
## GO:0005577 0.01119435 0.005740691 FN1 1
## ID
## GO:0004314 GO:0004314
## GO:0004315 GO:0004315
## GO:0004316 GO:0004316
## GO:0004345 GO:0004345
## GO:0004998 GO:0004998
## GO:0008659 GO:0008659
## Description
## GO:0004314 [acyl-carrier-protein] S-malonyltransferase activity
## GO:0004315 3-oxoacyl-[acyl-carrier-protein] synthase activity
## GO:0004316 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
## GO:0004345 glucose-6-phosphate dehydrogenase activity
## GO:0004998 transferrin receptor activity
## GO:0008659 (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity
## GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
## GO:0004314 1/6 2/18522 0.0006477907 0.003240407 0.0006541557 FASN 1
## GO:0004315 1/6 2/18522 0.0006477907 0.003240407 0.0006541557 FASN 1
## GO:0004316 1/6 2/18522 0.0006477907 0.003240407 0.0006541557 FASN 1
## GO:0004345 1/6 2/18522 0.0006477907 0.003240407 0.0006541557 G6PD 1
## GO:0004998 1/6 2/18522 0.0006477907 0.003240407 0.0006541557 TFRC 1
## GO:0008659 1/6 2/18522 0.0006477907 0.003240407 0.0006541557 FASN 1
## ID
## GO:0010039 GO:0010039
## GO:0044403 GO:0044403
## GO:0006953 GO:0006953
## GO:0002204 GO:0002204
## GO:0002208 GO:0002208
## GO:0045190 GO:0045190
## Description
## GO:0010039 response to iron ion
## GO:0044403 biological process involved in symbiotic interaction
## GO:0006953 acute-phase response
## GO:0002204 somatic recombination of immunoglobulin genes involved in immune response
## GO:0002208 somatic diversification of immunoglobulins involved in immune response
## GO:0045190 isotype switching
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0010039 2/6 28/18888 3.167154e-05 0.00792854 0.003156436
## GO:0044403 3/6 311/18888 8.523132e-05 0.00792854 0.003156436
## GO:0006953 2/6 47/18888 9.033104e-05 0.00792854 0.003156436
## GO:0002204 2/6 53/18888 1.150515e-04 0.00792854 0.003156436
## GO:0002208 2/6 53/18888 1.150515e-04 0.00792854 0.003156436
## GO:0045190 2/6 53/18888 1.150515e-04 0.00792854 0.003156436
## geneID Count
## GO:0010039 G6PD/TFRC 2
## GO:0044403 FN1/FASN/TFRC 3
## GO:0006953 FN1/TFRC 2
## GO:0002204 MSH6/TFRC 2
## GO:0002208 MSH6/TFRC 2
## GO:0045190 MSH6/TFRC 2
## ID Description GeneRatio BgRatio pvalue
## GO:0042470 GO:0042470 melanosome 2/6 112/19894 0.0004642992
## GO:0048770 GO:0048770 pigment granule 2/6 112/19894 0.0004642992
## GO:0032301 GO:0032301 MutSalpha complex 1/6 2/19894 0.0006031211
## GO:0072562 GO:0072562 blood microparticle 2/6 144/19894 0.0007657506
## GO:0042587 GO:0042587 glycogen granule 1/6 6/19894 0.0018084541
## GO:0005577 GO:0005577 fibrinogen complex 1/6 8/19894 0.0024106661
## p.adjust qvalue geneID Count
## GO:0042470 0.007466069 0.004030266 FASN/TFRC 2
## GO:0048770 0.007466069 0.004030266 FASN/TFRC 2
## GO:0032301 0.007466069 0.004030266 MSH6 1
## GO:0072562 0.007466069 0.004030266 FN1/TFRC 2
## GO:0042587 0.013430854 0.007250124 FASN 1
## GO:0005577 0.013430854 0.007250124 FN1 1
## ID
## GO:0016616 GO:0016616
## GO:0016614 GO:0016614
## GO:0004314 GO:0004314
## GO:0004315 GO:0004315
## GO:0004316 GO:0004316
## GO:0004345 GO:0004345
## Description
## GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
## GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
## GO:0004314 [acyl-carrier-protein] S-malonyltransferase activity
## GO:0004315 3-oxoacyl-[acyl-carrier-protein] synthase activity
## GO:0004316 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
## GO:0004345 glucose-6-phosphate dehydrogenase activity
## GeneRatio BgRatio pvalue p.adjust qvalue geneID
## GO:0016616 2/4 125/18522 0.0002687060 0.00141082 0.0001515382 G6PD/FASN
## GO:0016614 2/4 135/18522 0.0003133792 0.00141082 0.0001515382 G6PD/FASN
## GO:0004314 1/4 2/18522 0.0004318838 0.00141082 0.0001515382 FASN
## GO:0004315 1/4 2/18522 0.0004318838 0.00141082 0.0001515382 FASN
## GO:0004316 1/4 2/18522 0.0004318838 0.00141082 0.0001515382 FASN
## GO:0004345 1/4 2/18522 0.0004318838 0.00141082 0.0001515382 G6PD
## Count
## GO:0016616 2
## GO:0016614 2
## GO:0004314 1
## GO:0004315 1
## GO:0004316 1
## GO:0004345 1
## ID Description
## GO:0010039 GO:0010039 response to iron ion
## GO:0044403 GO:0044403 biological process involved in symbiotic interaction
## GO:0006953 GO:0006953 acute-phase response
## GO:0030099 GO:0030099 myeloid cell differentiation
## GO:0002526 GO:0002526 acute inflammatory response
## GO:0051702 GO:0051702 biological process involved in interaction with symbiont
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0010039 2/4 28/18888 1.269190e-05 0.003249522 0.001020648
## GO:0044403 3/4 311/18888 1.747055e-05 0.003249522 0.001020648
## GO:0006953 2/4 47/18888 3.624743e-05 0.004494682 0.001411742
## GO:0030099 3/4 439/18888 4.902361e-05 0.004559196 0.001432005
## GO:0002526 2/4 109/18888 1.965017e-04 0.013128987 0.004123706
## GO:0051702 2/4 119/18888 2.342272e-04 0.013128987 0.004123706
## geneID Count
## GO:0010039 G6PD/TFRC 2
## GO:0044403 FN1/FASN/TFRC 3
## GO:0006953 FN1/TFRC 2
## GO:0030099 G6PD/FASN/TFRC 3
## GO:0002526 FN1/TFRC 2
## GO:0051702 FN1/FASN 2
## ID Description GeneRatio BgRatio
## GO:0042470 GO:0042470 melanosome 2/4 112/19894
## GO:0048770 GO:0048770 pigment granule 2/4 112/19894
## GO:0072562 GO:0072562 blood microparticle 2/4 144/19894
## GO:0042587 GO:0042587 glycogen granule 1/4 6/19894
## GO:0005577 GO:0005577 fibrinogen complex 1/4 8/19894
## GO:1990712 GO:1990712 HFE-transferrin receptor complex 1/4 8/19894
## pvalue p.adjust qvalue geneID Count
## GO:0042470 0.0001870951 0.003461260 0.001477067 FASN/TFRC 2
## GO:0048770 0.0001870951 0.003461260 0.001477067 FASN/TFRC 2
## GO:0072562 0.0003092324 0.003813867 0.001627539 FN1/TFRC 2
## GO:0042587 0.0012059391 0.009914004 0.004230727 FASN 1
## GO:0005577 0.0016076763 0.009914004 0.004230727 FN1 1
## GO:1990712 0.0016076763 0.009914004 0.004230727 TFRC 1
## ID
## GO:0016616 GO:0016616
## GO:0016614 GO:0016614
## GO:0004314 GO:0004314
## GO:0004315 GO:0004315
## GO:0004316 GO:0004316
## GO:0004345 GO:0004345
## Description
## GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
## GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
## GO:0004314 [acyl-carrier-protein] S-malonyltransferase activity
## GO:0004315 3-oxoacyl-[acyl-carrier-protein] synthase activity
## GO:0004316 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
## GO:0004345 glucose-6-phosphate dehydrogenase activity
## GeneRatio BgRatio pvalue p.adjust qvalue geneID
## GO:0016616 2/4 125/18522 0.0002687060 0.00141082 0.0001515382 G6PD/FASN
## GO:0016614 2/4 135/18522 0.0003133792 0.00141082 0.0001515382 G6PD/FASN
## GO:0004314 1/4 2/18522 0.0004318838 0.00141082 0.0001515382 FASN
## GO:0004315 1/4 2/18522 0.0004318838 0.00141082 0.0001515382 FASN
## GO:0004316 1/4 2/18522 0.0004318838 0.00141082 0.0001515382 FASN
## GO:0004345 1/4 2/18522 0.0004318838 0.00141082 0.0001515382 G6PD
## Count
## GO:0016616 2
## GO:0016614 2
## GO:0004314 1
## GO:0004315 1
## GO:0004316 1
## GO:0004345 1
## ID Description
## GO:0010039 GO:0010039 response to iron ion
## GO:0044403 GO:0044403 biological process involved in symbiotic interaction
## GO:0006953 GO:0006953 acute-phase response
## GO:0030099 GO:0030099 myeloid cell differentiation
## GO:0002526 GO:0002526 acute inflammatory response
## GO:0051702 GO:0051702 biological process involved in interaction with symbiont
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0010039 2/4 28/18888 1.269190e-05 0.003249522 0.001020648
## GO:0044403 3/4 311/18888 1.747055e-05 0.003249522 0.001020648
## GO:0006953 2/4 47/18888 3.624743e-05 0.004494682 0.001411742
## GO:0030099 3/4 439/18888 4.902361e-05 0.004559196 0.001432005
## GO:0002526 2/4 109/18888 1.965017e-04 0.013128987 0.004123706
## GO:0051702 2/4 119/18888 2.342272e-04 0.013128987 0.004123706
## geneID Count
## GO:0010039 G6PD/TFRC 2
## GO:0044403 FN1/FASN/TFRC 3
## GO:0006953 FN1/TFRC 2
## GO:0030099 G6PD/FASN/TFRC 3
## GO:0002526 FN1/TFRC 2
## GO:0051702 FN1/FASN 2
## ID Description GeneRatio BgRatio
## GO:0042470 GO:0042470 melanosome 2/4 112/19894
## GO:0048770 GO:0048770 pigment granule 2/4 112/19894
## GO:0072562 GO:0072562 blood microparticle 2/4 144/19894
## GO:0042587 GO:0042587 glycogen granule 1/4 6/19894
## GO:0005577 GO:0005577 fibrinogen complex 1/4 8/19894
## GO:1990712 GO:1990712 HFE-transferrin receptor complex 1/4 8/19894
## pvalue p.adjust qvalue geneID Count
## GO:0042470 0.0001870951 0.003461260 0.001477067 FASN/TFRC 2
## GO:0048770 0.0001870951 0.003461260 0.001477067 FASN/TFRC 2
## GO:0072562 0.0003092324 0.003813867 0.001627539 FN1/TFRC 2
## GO:0042587 0.0012059391 0.009914004 0.004230727 FASN 1
## GO:0005577 0.0016076763 0.009914004 0.004230727 FN1 1
## GO:1990712 0.0016076763 0.009914004 0.004230727 TFRC 1
## ID
## GO:0016616 GO:0016616
## GO:0016614 GO:0016614
## GO:0004314 GO:0004314
## GO:0004315 GO:0004315
## GO:0004316 GO:0004316
## GO:0004345 GO:0004345
## Description
## GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
## GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
## GO:0004314 [acyl-carrier-protein] S-malonyltransferase activity
## GO:0004315 3-oxoacyl-[acyl-carrier-protein] synthase activity
## GO:0004316 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
## GO:0004345 glucose-6-phosphate dehydrogenase activity
## GeneRatio BgRatio pvalue p.adjust qvalue geneID
## GO:0016616 2/5 125/18522 0.0004458624 0.002463021 0.0003906738 G6PD/FASN
## GO:0016614 2/5 135/18522 0.0005198010 0.002463021 0.0003906738 G6PD/FASN
## GO:0004314 1/5 2/18522 0.0005398402 0.002463021 0.0003906738 FASN
## GO:0004315 1/5 2/18522 0.0005398402 0.002463021 0.0003906738 FASN
## GO:0004316 1/5 2/18522 0.0005398402 0.002463021 0.0003906738 FASN
## GO:0004345 1/5 2/18522 0.0005398402 0.002463021 0.0003906738 G6PD
## Count
## GO:0016616 2
## GO:0016614 2
## GO:0004314 1
## GO:0004315 1
## GO:0004316 1
## GO:0004345 1
## ID
## GO:0010039 GO:0010039
## GO:0044403 GO:0044403
## GO:0006953 GO:0006953
## GO:0002204 GO:0002204
## GO:0002208 GO:0002208
## GO:0045190 GO:0045190
## Description
## GO:0010039 response to iron ion
## GO:0044403 biological process involved in symbiotic interaction
## GO:0006953 acute-phase response
## GO:0002204 somatic recombination of immunoglobulin genes involved in immune response
## GO:0002208 somatic diversification of immunoglobulins involved in immune response
## GO:0045190 isotype switching
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0010039 2/5 28/18888 2.113375e-05 0.00436869 0.001521082
## GO:0044403 3/5 311/18888 4.314255e-05 0.00436869 0.001521082
## GO:0006953 2/5 47/18888 6.031646e-05 0.00436869 0.001521082
## GO:0002204 2/5 53/18888 7.683924e-05 0.00436869 0.001521082
## GO:0002208 2/5 53/18888 7.683924e-05 0.00436869 0.001521082
## GO:0045190 2/5 53/18888 7.683924e-05 0.00436869 0.001521082
## geneID Count
## GO:0010039 G6PD/TFRC 2
## GO:0044403 FN1/FASN/TFRC 3
## GO:0006953 FN1/TFRC 2
## GO:0002204 MSH6/TFRC 2
## GO:0002208 MSH6/TFRC 2
## GO:0045190 MSH6/TFRC 2
## ID Description GeneRatio BgRatio pvalue
## GO:0042470 GO:0042470 melanosome 2/5 112/19894 0.0003106766
## GO:0048770 GO:0048770 pigment granule 2/5 112/19894 0.0003106766
## GO:0032301 GO:0032301 MutSalpha complex 1/5 2/19894 0.0005026136
## GO:0072562 GO:0072562 blood microparticle 2/5 144/19894 0.0005129374
## GO:0042587 GO:0042587 glycogen granule 1/5 6/19894 0.0015072345
## GO:0005577 GO:0005577 fibrinogen complex 1/5 8/19894 0.0020092419
## p.adjust qvalue geneID Count
## GO:0042470 0.00500114 0.002564687 FASN/TFRC 2
## GO:0048770 0.00500114 0.002564687 FASN/TFRC 2
## GO:0032301 0.00500114 0.002564687 MSH6 1
## GO:0072562 0.00500114 0.002564687 FN1/TFRC 2
## GO:0042587 0.01119435 0.005740691 FASN 1
## GO:0005577 0.01119435 0.005740691 FN1 1
## ID
## GO:0004314 GO:0004314
## GO:0004315 GO:0004315
## GO:0004316 GO:0004316
## GO:0004345 GO:0004345
## GO:0004998 GO:0004998
## GO:0008659 GO:0008659
## Description
## GO:0004314 [acyl-carrier-protein] S-malonyltransferase activity
## GO:0004315 3-oxoacyl-[acyl-carrier-protein] synthase activity
## GO:0004316 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
## GO:0004345 glucose-6-phosphate dehydrogenase activity
## GO:0004998 transferrin receptor activity
## GO:0008659 (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity
## GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
## GO:0004314 1/6 2/18522 0.0006477907 0.003240407 0.0006541557 FASN 1
## GO:0004315 1/6 2/18522 0.0006477907 0.003240407 0.0006541557 FASN 1
## GO:0004316 1/6 2/18522 0.0006477907 0.003240407 0.0006541557 FASN 1
## GO:0004345 1/6 2/18522 0.0006477907 0.003240407 0.0006541557 G6PD 1
## GO:0004998 1/6 2/18522 0.0006477907 0.003240407 0.0006541557 TFRC 1
## GO:0008659 1/6 2/18522 0.0006477907 0.003240407 0.0006541557 FASN 1
## ID
## GO:0010039 GO:0010039
## GO:0044403 GO:0044403
## GO:0006953 GO:0006953
## GO:0002204 GO:0002204
## GO:0002208 GO:0002208
## GO:0045190 GO:0045190
## Description
## GO:0010039 response to iron ion
## GO:0044403 biological process involved in symbiotic interaction
## GO:0006953 acute-phase response
## GO:0002204 somatic recombination of immunoglobulin genes involved in immune response
## GO:0002208 somatic diversification of immunoglobulins involved in immune response
## GO:0045190 isotype switching
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0010039 2/6 28/18888 3.167154e-05 0.00792854 0.003156436
## GO:0044403 3/6 311/18888 8.523132e-05 0.00792854 0.003156436
## GO:0006953 2/6 47/18888 9.033104e-05 0.00792854 0.003156436
## GO:0002204 2/6 53/18888 1.150515e-04 0.00792854 0.003156436
## GO:0002208 2/6 53/18888 1.150515e-04 0.00792854 0.003156436
## GO:0045190 2/6 53/18888 1.150515e-04 0.00792854 0.003156436
## geneID Count
## GO:0010039 G6PD/TFRC 2
## GO:0044403 FN1/FASN/TFRC 3
## GO:0006953 FN1/TFRC 2
## GO:0002204 MSH6/TFRC 2
## GO:0002208 MSH6/TFRC 2
## GO:0045190 MSH6/TFRC 2
## ID Description GeneRatio BgRatio pvalue
## GO:0042470 GO:0042470 melanosome 2/6 112/19894 0.0004642992
## GO:0048770 GO:0048770 pigment granule 2/6 112/19894 0.0004642992
## GO:0032301 GO:0032301 MutSalpha complex 1/6 2/19894 0.0006031211
## GO:0072562 GO:0072562 blood microparticle 2/6 144/19894 0.0007657506
## GO:0042587 GO:0042587 glycogen granule 1/6 6/19894 0.0018084541
## GO:0005577 GO:0005577 fibrinogen complex 1/6 8/19894 0.0024106661
## p.adjust qvalue geneID Count
## GO:0042470 0.007466069 0.004030266 FASN/TFRC 2
## GO:0048770 0.007466069 0.004030266 FASN/TFRC 2
## GO:0032301 0.007466069 0.004030266 MSH6 1
## GO:0072562 0.007466069 0.004030266 FN1/TFRC 2
## GO:0042587 0.013430854 0.007250124 FASN 1
## GO:0005577 0.013430854 0.007250124 FN1 1
## ID
## GO:0016616 GO:0016616
## GO:0016614 GO:0016614
## GO:0004314 GO:0004314
## GO:0004315 GO:0004315
## GO:0004316 GO:0004316
## GO:0004345 GO:0004345
## Description
## GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
## GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
## GO:0004314 [acyl-carrier-protein] S-malonyltransferase activity
## GO:0004315 3-oxoacyl-[acyl-carrier-protein] synthase activity
## GO:0004316 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
## GO:0004345 glucose-6-phosphate dehydrogenase activity
## GeneRatio BgRatio pvalue p.adjust qvalue geneID
## GO:0016616 2/4 125/18522 0.0002687060 0.00141082 0.0001515382 G6PD/FASN
## GO:0016614 2/4 135/18522 0.0003133792 0.00141082 0.0001515382 G6PD/FASN
## GO:0004314 1/4 2/18522 0.0004318838 0.00141082 0.0001515382 FASN
## GO:0004315 1/4 2/18522 0.0004318838 0.00141082 0.0001515382 FASN
## GO:0004316 1/4 2/18522 0.0004318838 0.00141082 0.0001515382 FASN
## GO:0004345 1/4 2/18522 0.0004318838 0.00141082 0.0001515382 G6PD
## Count
## GO:0016616 2
## GO:0016614 2
## GO:0004314 1
## GO:0004315 1
## GO:0004316 1
## GO:0004345 1
## ID Description
## GO:0010039 GO:0010039 response to iron ion
## GO:0044403 GO:0044403 biological process involved in symbiotic interaction
## GO:0006953 GO:0006953 acute-phase response
## GO:0030099 GO:0030099 myeloid cell differentiation
## GO:0002526 GO:0002526 acute inflammatory response
## GO:0051702 GO:0051702 biological process involved in interaction with symbiont
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0010039 2/4 28/18888 1.269190e-05 0.003249522 0.001020648
## GO:0044403 3/4 311/18888 1.747055e-05 0.003249522 0.001020648
## GO:0006953 2/4 47/18888 3.624743e-05 0.004494682 0.001411742
## GO:0030099 3/4 439/18888 4.902361e-05 0.004559196 0.001432005
## GO:0002526 2/4 109/18888 1.965017e-04 0.013128987 0.004123706
## GO:0051702 2/4 119/18888 2.342272e-04 0.013128987 0.004123706
## geneID Count
## GO:0010039 G6PD/TFRC 2
## GO:0044403 FN1/FASN/TFRC 3
## GO:0006953 FN1/TFRC 2
## GO:0030099 G6PD/FASN/TFRC 3
## GO:0002526 FN1/TFRC 2
## GO:0051702 FN1/FASN 2
## ID Description GeneRatio BgRatio
## GO:0042470 GO:0042470 melanosome 2/4 112/19894
## GO:0048770 GO:0048770 pigment granule 2/4 112/19894
## GO:0072562 GO:0072562 blood microparticle 2/4 144/19894
## GO:0042587 GO:0042587 glycogen granule 1/4 6/19894
## GO:0005577 GO:0005577 fibrinogen complex 1/4 8/19894
## GO:1990712 GO:1990712 HFE-transferrin receptor complex 1/4 8/19894
## pvalue p.adjust qvalue geneID Count
## GO:0042470 0.0001870951 0.003461260 0.001477067 FASN/TFRC 2
## GO:0048770 0.0001870951 0.003461260 0.001477067 FASN/TFRC 2
## GO:0072562 0.0003092324 0.003813867 0.001627539 FN1/TFRC 2
## GO:0042587 0.0012059391 0.009914004 0.004230727 FASN 1
## GO:0005577 0.0016076763 0.009914004 0.004230727 FN1 1
## GO:1990712 0.0016076763 0.009914004 0.004230727 TFRC 1
## ID
## GO:0016616 GO:0016616
## GO:0016614 GO:0016614
## GO:0004314 GO:0004314
## GO:0004315 GO:0004315
## GO:0004316 GO:0004316
## GO:0004345 GO:0004345
## Description
## GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
## GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
## GO:0004314 [acyl-carrier-protein] S-malonyltransferase activity
## GO:0004315 3-oxoacyl-[acyl-carrier-protein] synthase activity
## GO:0004316 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
## GO:0004345 glucose-6-phosphate dehydrogenase activity
## GeneRatio BgRatio pvalue p.adjust qvalue geneID
## GO:0016616 2/4 125/18522 0.0002687060 0.00141082 0.0001515382 G6PD/FASN
## GO:0016614 2/4 135/18522 0.0003133792 0.00141082 0.0001515382 G6PD/FASN
## GO:0004314 1/4 2/18522 0.0004318838 0.00141082 0.0001515382 FASN
## GO:0004315 1/4 2/18522 0.0004318838 0.00141082 0.0001515382 FASN
## GO:0004316 1/4 2/18522 0.0004318838 0.00141082 0.0001515382 FASN
## GO:0004345 1/4 2/18522 0.0004318838 0.00141082 0.0001515382 G6PD
## Count
## GO:0016616 2
## GO:0016614 2
## GO:0004314 1
## GO:0004315 1
## GO:0004316 1
## GO:0004345 1
## ID Description
## GO:0010039 GO:0010039 response to iron ion
## GO:0044403 GO:0044403 biological process involved in symbiotic interaction
## GO:0006953 GO:0006953 acute-phase response
## GO:0030099 GO:0030099 myeloid cell differentiation
## GO:0002526 GO:0002526 acute inflammatory response
## GO:0051702 GO:0051702 biological process involved in interaction with symbiont
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0010039 2/4 28/18888 1.269190e-05 0.003249522 0.001020648
## GO:0044403 3/4 311/18888 1.747055e-05 0.003249522 0.001020648
## GO:0006953 2/4 47/18888 3.624743e-05 0.004494682 0.001411742
## GO:0030099 3/4 439/18888 4.902361e-05 0.004559196 0.001432005
## GO:0002526 2/4 109/18888 1.965017e-04 0.013128987 0.004123706
## GO:0051702 2/4 119/18888 2.342272e-04 0.013128987 0.004123706
## geneID Count
## GO:0010039 G6PD/TFRC 2
## GO:0044403 FN1/FASN/TFRC 3
## GO:0006953 FN1/TFRC 2
## GO:0030099 G6PD/FASN/TFRC 3
## GO:0002526 FN1/TFRC 2
## GO:0051702 FN1/FASN 2
## ID Description GeneRatio BgRatio
## GO:0042470 GO:0042470 melanosome 2/4 112/19894
## GO:0048770 GO:0048770 pigment granule 2/4 112/19894
## GO:0072562 GO:0072562 blood microparticle 2/4 144/19894
## GO:0042587 GO:0042587 glycogen granule 1/4 6/19894
## GO:0005577 GO:0005577 fibrinogen complex 1/4 8/19894
## GO:1990712 GO:1990712 HFE-transferrin receptor complex 1/4 8/19894
## pvalue p.adjust qvalue geneID Count
## GO:0042470 0.0001870951 0.003461260 0.001477067 FASN/TFRC 2
## GO:0048770 0.0001870951 0.003461260 0.001477067 FASN/TFRC 2
## GO:0072562 0.0003092324 0.003813867 0.001627539 FN1/TFRC 2
## GO:0042587 0.0012059391 0.009914004 0.004230727 FASN 1
## GO:0005577 0.0016076763 0.009914004 0.004230727 FN1 1
## GO:1990712 0.0016076763 0.009914004 0.004230727 TFRC 1barplot(ego_MF[[1]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, Multigroup")
barplot(ego_MF[[2]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, Onegroup")
barplot(ego_MF[[3]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 1, Multigroup")
barplot(ego_MF[[4]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 1, Multigroup")
barplot(ego_MF[[5]], title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, Multigroup")
barplot(ego_MF[[6]], title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, Onegroup")
barplot(ego_MF[[7]], title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 1, Multigroup")
barplot(ego_MF[[8]], title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 1, Onegroup")
barplot(ego_MF[[9]], title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Multigroup")
barplot(ego_MF[[10]], title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Onegroup")
barplot(ego_MF[[11]], title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 1, Multigroup")
barplot(ego_MF[[12]], title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 1, Onegroup")
barplot(ego_BP[[1]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, Multigroup")
barplot(ego_BP[[2]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, Onegroup")
barplot(ego_BP[[3]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 1, Multigroup")
barplot(ego_BP[[4]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 1, Multigroup")
barplot(ego_BP[[5]], title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 0.5, Multigroup")
barplot(ego_BP[[6]], title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 0.5, Onegroup")
barplot(ego_BP[[7]], title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 1, Multigroup")
barplot(ego_BP[[8]], title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 1, Onegroup")
barplot(ego_BP[[9]], title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Multigroup")
barplot(ego_BP[[10]], title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Onegroup")
barplot(ego_BP[[11]], title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 1, Multigroup")
barplot(ego_BP[[12]], title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 1, Onegroup")
barplot(ego_CC[[1]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, Multigroup")
barplot(ego_CC[[2]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, Onegroup")
barplot(ego_CC[[3]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 1, Multigroup")
barplot(ego_CC[[4]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 1, Multigroup")
barplot(ego_CC[[5]], title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, Multigroup")
barplot(ego_CC[[6]], title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, Onegroup")
barplot(ego_CC[[7]], title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 1, Multigroup")
barplot(ego_CC[[8]], title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 1, Onegroup")
barplot(ego_CC[[9]], title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Multigroup")
barplot(ego_CC[[10]], title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Onegroup")
barplot(ego_CC[[11]], title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 1, Multigroup")
barplot(ego_CC[[12]], title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 1, Onegroup")
DAG plots for ego
goplot(ego_MF[[1]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, Multigroup")
goplot(ego_MF[[2]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, Onegroup")
goplot(ego_MF[[3]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 1, Multigroup")
goplot(ego_MF[[4]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 1, Multigroup")
goplot(ego_MF[[5]]) + labs(title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, Multigroup")
goplot(ego_MF[[6]]) + labs(title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, Onegroup")
goplot(ego_MF[[7]]) + labs(title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 1, Multigroup")
goplot(ego_MF[[8]]) + labs(title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 1, Onegroup")
goplot(ego_MF[[9]]) + labs(title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Multigroup")
goplot(ego_MF[[10]]) + labs(title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Onegroup")
goplot(ego_MF[[11]]) + labs(title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 1, Multigroup")
goplot(ego_MF[[12]]) + labs(title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 1, Onegroup")
goplot(ego_BP[[1]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, Multigroup")## Warning: ggrepel: 1 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[2]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, Onegroup")
goplot(ego_BP[[3]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 1, Multigroup")
goplot(ego_BP[[4]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 1, Multigroup")
goplot(ego_BP[[5]]) + labs(title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 0.5, Multigroup")## Warning: ggrepel: 1 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[6]]) + labs(title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 0.5, Onegroup")
goplot(ego_BP[[7]]) + labs(title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 1, Multigroup")
goplot(ego_BP[[8]]) + labs(title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 1, Onegroup")
goplot(ego_BP[[9]]) + labs(title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Multigroup")## Warning: ggrepel: 1 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[10]]) + labs(title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Onegroup")
goplot(ego_BP[[11]]) + labs(title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 1, Multigroup")
goplot(ego_BP[[12]]) + labs(title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 1, Onegroup")
goplot(ego_CC[[1]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, Multigroup")
goplot(ego_CC[[2]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, Onegroup")
goplot(ego_CC[[3]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 1, Multigroup")
goplot(ego_CC[[4]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 1, Multigroup")
goplot(ego_CC[[5]]) + labs(title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, Multigroup")
goplot(ego_CC[[6]]) + labs(title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, Onegroup")
goplot(ego_CC[[7]]) + labs(title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 1, Multigroup")
goplot(ego_CC[[8]]) + labs(title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 1, Onegroup")
goplot(ego_CC[[9]]) + labs(title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Multigroup")
goplot(ego_CC[[10]]) + labs(title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Onegroup")
goplot(ego_CC[[11]]) + labs(title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 1, Multigroup")
goplot(ego_CC[[12]]) + labs(title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 1, Onegroup")
3. Export Pathway Analysis result to data
pathway = list("ggo_MF" = ggo_MF,
"ggo_BP" = ggo_BP,
"ggo_CC" = ggo_CC,
"ego_MF" = ego_MF,
"ego_BP" = ego_BP,
"ego_CC" = ego_CC)
saveRDS(pathway, file = "data/out_pathway/pathways_squeezy.rds")